I’m using keyboard shortcut extensively and never experienced your reported behaviour.
In addition, I would expect to see more threads like yours if this is a general issue of npp.
So I think it must be related to your special setup. I have a few questions which might help
to find out what is going on.

Because you are saying

mainly working on java-script language

I’m under the impression that it happens not only be using java script language but when using npp in general, is this correct?
Does it also happen with other windows software?
Are you using windows operating system nativley or any virtualization software like VM player, virtualbox, sandbox etc… running npp?
Did it start happening after installing npp or was it working for some time and suddenly it started to break?
Where some changes in soft- and hardware done recently (in regards to when it start to happen)?
Do you use a global keyboard shortcut mapper? (software which register keyboard shortcuts globally instead of per application (focused))?

Currently observed that it happens when i start the npp.( i have tried to close and again start the npp to check whether short-cuts start working but it doesn’t work ) All the short-cuts not working. Then I have re install it. After re-installation with default setting i just change the language option and select Java script. This is the only change i have made in default setting.

Note :: But when i change the language setting like selecting java language or Action-script it start working but when i select again Java Script as language it is not working…